Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
BMC Genomics. 2019 Feb 13;20(1):132. doi: 10.1186/s12864-019-5444-4.
Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes.
In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis.
The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.
陆地植物细胞器基因组对代谢和适应有重大影响，因此，准确组装和注释植物细胞器基因组是理解这些基因组的进化历史和相互作用的重要工具。核基因组和细胞器基因组之间存在着持续的胞内 DNA 转移，这会导致物种之间以及物种内部的基因组发生显著变异，从而影响对基因组和转录组的下游分析。
为了促进桉树胞质-核相互作用的进一步研究，我们报告了一个经过更新的大果桉质体基因组注释，以及桃金娘目第二个测序和注释的线粒体基因组，即大果桉的线粒体基因组。该 478813bp 的线粒体基因组显示出陆地植物典型的保守蛋白编码区和基因顺序重排。广泛存在的细胞器 DNA 插入到大果桉核基因组中，跨越了 141 个注释核基因。此外，我们还鉴定了预测的编辑位点，以区分核基因和细胞器基因的 RNA-seq 读段，发现大果桉核基因的细胞器基因拷贝不表达。
尽管细胞器 DNA 转移到细胞核可以深入了解植物基因组的持续进化，以及它们在许多基因组学应用中可能引发的问题，但它们的影响往往被忽视。未来对桉树基因型间细胞器基因的转录和调控的比较，可能为影响这一广泛种植的木质纤维素作物物种中经济重要性状的胞质-核相互作用提供启示。
